Lets not forget Desmond was trying to make up with Pen and since Whitmore gave him her address.. He knew where to get her letters from if he didn't have the prison saving them for him to give back to Desmond when he is freed... So Penny doesn't know that he was writting her.. When did she put the letter in the book? The one he wasn't going to read until he was going to die?

I would have to say after he is put in prison, she wanted him to find it in there.. He never did so all the events continued on..

__________________
Please don't give up, Des. Because all we really need to survive is one person who truly loves us. And you have her. I will wait for
you. Always. I love you, Pen

DESMOND: I love you, Penny. I've always loved you. I'm so sorry. I love you!
PENNY: I love you too.
DESMOND: I don't know where I am, but--
PENNY: I'll find you, Des--
DESMOND: --I promise--
PENNY: --no matter what--
DESMOND: --I'll come back to you--
PENNY: --I won't give up--
BOTH: I promise. I love you.